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length_seq
Martin Asser Hansen edited this page Oct 2, 2015
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length_seq determines the length of each sequence in the stream and add this to the
SEQ_LEN key.
... | length_seq [options]
[-? | --help] # Print full usage description.
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to file - Default=STDOUT
[-v | --verbose] # Verbose output.
Consider the following table in the file test.tab:
#SEQ_NAME SEQ
test1 ACGACGAGCATGCA
test2 ACGACTACCTG
We can read in this table using read_tab and then pipe the stream though length_seq:
read_tab -i test.tab | length_seq
SEQ: ACGACGAGCATGCA
SEQ_NAME: test1
SEQ_LEN: 14
---
SEQ: ACGACTACCTG
SEQ_NAME: test2
SEQ_LEN: 11
---
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
length_seq is part of the Biopieces framework.